[gmx-users] topology defaults directive

[Berk Hess]

>I tried using gen-pairs=yes and generating a pairtypes list for certain 1-4
>LJ interactions in a molecule.itp file. I listed the pairtypes directly
>below the atomtypes section.  However, grompp complained about
>all of the pairtypes in the list, giving
>
>WARNING 1 [file "ffoplsaa_lipidnb.itp", line 737]:
>   Trying to add LJ-14 while the default nonbond type is LJ (SR)
>WARNING 2 [file "ffoplsaa_lipidnb.itp", line 738]:
>   Trying to add LJ-14 while the default nonbond type is LJ (SR)
>etc.
>etc.
>
>Perhaps this means that the only choice is to list the interactions under
>the pairs section?

You should ignore these warnings (use the -maxwarn option if there are too 
many).
I'll remove the warning in the next release.

You can check the final parameters by using gmxdump -s or gmxcheck -s1 -s2
on your tpr files.

Berk.

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